Misconceptions
by Ren201
Summary: Alternative view to how Sydney could have returned to the CIA. R&R. Pairing will be revealed at the end of the 1st chapter. Nothing is ever simple in my stories, you have been warned!
1. Double Agent

Title: Misconceptions  
  
Author: Ren201  
  
Spoilers: Up to 'The Telling' (end of season 2) but a different ending. Sydney was still 'missing' but returned in a different way.  
  
Disclaimer: I don't own anything to do with Alias or anything else that doesn't belong to me.  
  
Author's note: This story was originally called something else, but I didn't like it, so I've changed the title and (hopefully) improved what I wrote. In fact, this is nothing like the original story, so it doesn't really matter. lol.  
  
A/N: R&R please.  
  
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Sydney Bristow sat impatiently in the conference room, awaiting the arrival of the agents who were to be involved in her case. Sighing, she watched as the agents began to file into the room, all unaware of the reason they were there.  
  
Many agents didn't recognise her and sent her inquisitive stares, but the few who did, were shocked to see that she was still alive. Before any of the agents could approach her, Dixon entered the room, causing everyone to take their respective seats.  
  
Sydney stood as Dixon entered the room, and moved towards him, pulling him into a quick embrace.  
  
"It's good to see you again. Two months is too long." Sydney said as she pulled away from him.  
  
All eyes moved onto Sydney again, as she subconsciously, placed a hand over her swollen stomach, as if she were protecting it from the people around her. Sydney looked briefly at the agents before her, as she straighten her business suit, noticing one in particular. Michael Vaughn. The thing stood out the most about him, was the wedding ring on his finger. Avoiding his gaze, she moved back towards her seat, to wait for Dixon to continue with the briefing.  
  
"Agent Sydney Bristow has been undercover within the Covenant since her kidnapping two years ago." Dixon stated as he began handing out folders containing information on Sydney's double agent status, before motioning to Sydney, who reluctantly stood and moved towards the screen at the front of the room to continue with the briefing.  
  
"I've been working as an operative within the Covenant for the past 15 months. The main objective of my work has been to destroy the Covenant and obtain the relevant information needed to do this." Sydney stated as she once again placed her hand over her stomach before continuing.  
  
"The work I've been doing was complicated and dangerous. It was not by choice that I joined the Covenant. They believed that they had successfully brainwashed me, which meant that they had no reason to doubt my loyalty. This gave me the opportunity to become a double agent." Sydney said, as she waited for the agents to finish looking through her file.  
  
"Why did you come back now? Why not stay within the Covenant until the end of your pregnancy to ensure that they completely trusted you? How far along are you?" A female agent asked, as she motioned to Sydney's stomach.  
  
"Almost 7 months." Sydney replied briefly smiled down at her stomach.  
  
"The main reason for my extraction was due to my pregnancy, but not for the reasons you would think Agent...". Sydney replied, trailing off.  
  
"Jackson. What do you mean?" Agent Jackson replied as she closed her folder, giving all of her attention to Sydney.  
  
"There is a prophecy that many believe was written about me. When the CIA first discovered the prophecy, it was presumed that it only concerned me. Unfortunately, the Covenant received Intel about another page from the Rambaldi manuscript. This page described both a man and a child.  
  
"It wasn't until a few months ago that I found out about the page. Due to the Covenant's belief that I was brainwashed, they were under the impression that I hadn't seen the first part of the prophecy. Since that time, we have been working to retrieve the manuscript page and discover the meaning behind the prophecy." Sydney concluded as she allowed the agents to ask their questions.  
  
"If you didn't know about the prophecy until after you were pregnant, then how were the Covenant able to ensure that your pregnancy would happen the way it was predicted?" Weiss asked as he gave Sydney a sympathetic look and a small smile.  
  
"I don't know. Although I assume that the main reason they abducted me was to for fill this prophecy. I would assume that they knew about both pages, as my partner within the Covenant was the man in the prophecy." Sydney replied as she briefly looked towards Dixon, looking for confirmation of what she could tell the agents.  
  
"What was the prophecy?" A young blonde woman asked in a crisp British accent, as she looked towards Sydney.  
  
"I was never given that information, which is why we need to acquire the page, Ms Reed." Sydney replied as she looked directly at her, waiting for her response before she continued,  
  
"Congratulations by the way. I hear the wedding was nice." Sydney concluded as she looked at both Vaughn and his wife before moving back to her seat. Feeling the tension rise in the room, Sydney was satisfied that no one else would ask her any more questions.  
  
"Who was the man in the prophecy?" Vaughn asked gingerly, as he avoided eye contact, deciding instead to look at his hands.  
  
"Why?" Sydney replied as she turned to face him again, ignoring the uncomfortable silence that surrounded the rest of the agents.  
  
"If we are going to bring down the Covenant we need to know the details. We need to know who is working with us and who is working against us." Vaughn replied as he briefly looked round the room at the other agents.  
  
"The man in the prophecy was ... Julian Lazarey, ... but you know him as Sark." Sydney announced, as she sat down again, placing her hand lovingly over her stomach.  
  
~#~#~#~#~  
  
This wasn't as well written, as I would have hoped, but R&R anyway. Sorry to all Syd/Vaughn shippers who thought that this would be S/V, but I didn't want to ruin the surprise. 


	2. Donuts and manuscripts

Title: Misconceptions  
  
Author: Ren201  
  
Spoilers: Up to 'The Telling' (end of season 2) but a different ending. Sydney was still 'missing' but returned in a different way, Sark was never in CIA custody during the past two years.  
  
Disclaimer: I don't own anything to do with Alias or anything else that doesn't belong to me.  
  
Author's note: Sorry that this has taken so long for me to update. So here's the next chapter for everyone who's reading! Thanks for the reviews!  
  
A/N: I'm not sure how I'm doing on this fic, so I think I'm looking for a beta. (Although, to be completely honest, I'm 100% what jobs a beta does other than checking through the chapter, if any.)  
  
Any volunteers? E-mail me or review. Thanks. .  
  
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"The man in the prophecy was ... Julian Lazarey, ... but you know him as Sark." Sydney announced, as she sat down again, placing her hand lovingly over her stomach.  
  
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Sydney couldn't help but smirk, something that she had picked up from Sark, when she saw the looks she was receiving. She knew that this was the last thing that anyone was expecting. With the exception of Dixon, everyone in the room was completely stunned by her announcement.  
  
Looking towards Vaughn, Sydney could see the hurt and shock he felt. It shone through his eyes and for a brief moment, Sydney regretted what had happened the last two years. Then she remembered what she had with Sark. It was so different to what she had had with Vaughn. She couldn't even begin to compare the two men; they were two completely different people.  
  
She had been so in love with Vaughn that it hurt to breathe without him, but Vaughn had given up on her, he had lost faith; he had betrayed her.  
  
Then there was Sark, he had saved her so many times, in so many different ways that she couldn't help but fall in love with him. He had done so much and given up more than he should have for her. She had seen a completely different side to him; a side to him reserved only for her.  
  
There was a time when she honestly believed that Vaughn was her soul mate, and that it was their destiny to be together. Oh how wrong she had been; if she had known then what she knows now, things would have been so different.  
  
She would have thought their situation to be strangely ironic if it weren't so complicated. She knew how Vaughn felt, but she refused to show him how he had effected her and the control he still had over her.  
  
There were very few people who knew of Sydney's relationship with Sark, namely, her father, Dixon and Kendal, as well as members of the Covenant and a few higher ups within the CIA. They had all decided that there was too much risk to 'inform' anyone else of their 'connection' as they called it.  
  
"How did this happen?" Vaughn eventually asked after finding his voice again, feeling completely confused by what he had just heard. He didn't believe that Sydney would willingly carry Sark's child, it just didn't make any sense.  
  
"Do you really need me to tell you how women get pregnant Vaughn?" Sydney asked with a hint of humour in her voice, trying to avoid the subject.  
  
"No, of course not. I mean ... how did this happen? What made you do this?" Vaughn replied slightly dazed, surprised by her response. This wasn't the Sydney he knew and loved.  
  
"What can I say? Six months of torture and 're-education' changes a person. There are things that you would never understand and I'm not going to explain myself to you, and I'm not asking for you to do that either.  
  
"Things change, and coming home to find your boyfriend with another women nine months after your 'death' wasn't exactly something that would encourage you to return home, now is it?" Sydney responded, as she let out a long sigh, looking towards Dixon, before changing the subject, hoping to avoid any questions that would inevitably be asked about Sark.  
  
"That isn't the point. There are more relevant issues that need to be dealt with." Sydney continued as she looked over the faces of the agents before her, trying to ignore Vaughn and his wife, surprised at the sense of betrayal she still felt.  
  
Wiping all of her thoughts from her mind, Sydney moved back towards the table and opening a bottle of water, taking a quick sip before carrying on,  
  
"When I said that I had been extracted, that wasn't entirely accurate. I still work for the Covenant and they expect me to return, I only have a limited amount of time before they become suspicious. My pregnancy has given me some leeway, but Sark can only cover for me for a certain amount of time." Sydney stated, placing a hand behind her back, trying to support her aching muscles by relieving her back of some of the extra weight.  
  
"How does Sark fit in with all of this, I mean other than the prophecy. Is he working with us or against?" Agent Jackson asked curiously  
  
"He's working with us and has been for the past 15 months. He wants to take down the Covenant as much as we do." Sydney replied as she felt her body become restless once again.  
  
"We should have more Intel on the Rambaldi manuscript soon, Sark is currently working on the location. He should be contacting us within the hour with the information we need. From what we already know the manuscript will be transferred to the LA branch of the Covenant from the Russia some time tomorrow. It is too risky to intercept the document before it arrives in LA." Sydney confirmed and was about to continue when she was interrupted by the sound of her cell phone ringing from her jacket packet.  
  
Immediately pulling out her cell, she answered the call.  
  
"Julia Thorne." Sydney stated confidently as she watched the agent's reaction to the use of her alias.  
  
"Hi." Sydney replied into her cell phone as she smiled and placed her free hand over her stomach.  
  
"Why? What happened?" Sydney immediately questioned, as her voice suddenly filled with apprehension. Moving slightly towards the door, Sydney waited impatiently for the caller to explain what was wrong.  
  
The agents in the room were intrigued by the call and annoyed at the same time that they could only hear one side of the conversation. They watched as the apprehension drained from Sydney's face and was replaced by relief.  
  
Letting out a breath that she didn't know that she was holding, Sydney replied to the caller's statement.  
  
"You mean now? Where are you?" Patience was not one of Sydney Bristow's qualities and while listening to the caller's voice; Sydney quickly moved towards her bag and pulled out her car keys.  
  
"I'll meet you. Just wait there for me, ok?" Sydney replied urgently.  
  
"I'm leaving now, so just wait." Sydney replied as she quietly chuckled to the caller's response.  
  
"Yeah, a donut would be great right about now. Hold on a second." Sydney replied as she paused, placing her hand over her phone, turning towards the group of agents in front of her.  
  
"There's been a change of plan ... I need to collect something that will help us with the operation. If you look over the mission specs while I'm gone and catch up with any information that you might need and then we can go over the mission when I get back." Sydney said as she moved towards Dixon  
  
"I won't be long, just keep everyone here so we can continue when I get back, ok." Sydney concluded as she placed her phone back to her ear and carried on speaking to the caller.  
  
"So are you going to get me that donut, because now that you've said it, I could really eat a chocolate donut from that place down the road." Sydney replied as she opened the door and quickly walked out. The last thing the agents in the room heard was the sound of Sydney laughing as she walked along the corridor before the doors closed.  
  
~*~*~  
  
Vaughn felt incredibly jealous. He had never felt this way before and hoped that he would never feel this way again. He knew that he had no right to feel like this, after all, it was his fault that Sydney had became a double agent. He couldn't blame her for moving on, he had. Only, now, he was regretting marrying Lauren. He couldn't help but think of what he had lost ... again. He could have changed this. Things could have been so different.  
  
Vaughn listened enviously as Sydney had a normal conversation, he listened as she laughed and talked about wanting to eat a donut. That was thing that struck him the most about the conversation, the donut. That was the kind of stuff he should be laughing about with Sydney. It should have been him with them memories of the 'donut place'; he should be the man who knew about her cravings for chocolate donuts and could tease her about them.  
  
It was killing him that he wasn't that the person on the other end of phone, but more than that, it was killing him noting know what the other person was saying.  
  
He had listened intently to everything that Sydney had said, and yet he still hadn't processed any of it. He was still finding it hard to accept that she was alive, he spread her ashes at sea. She had died.  
  
Vaughn spent the next 25 minutes trying to memorise all of the information that he possibly could before Sydney came back. He needed to know everything that he could about her missing time. There was no way he would sit back and watch Sydney from afar. It was true that he had Lauren now, but he needed to be near Sydney, and he would do whatever he could to make that happen.  
  
~*~*~  
  
As the conference room door opened, 25 minutes after Sydney had left, a sudden realisation hit Vaughn. Sydney was talking to Sark on the phone before she left, and she had gone to pick him up. Vaughn suddenly felt his heart plummet and his stomach tighten as he saw Sydney enter the room.  
  
~*~*~  
  
As Sydney approached the door to the conference room, she stopped and turned towards Sark. They had received many strange looks from the agents in the bullpen on their way towards the conference room, and Sydney suddenly felt a surge of anxiety.  
  
"Are you sure you want to do this?" Sydney asked suddenly, looking into Sark's eyes.  
  
"Of course. This isn't a problem Syd; we've handled worse then this. Do you not remember Ireland?" Sark asked with a hint of humour in his eyes.  
  
Sydney merely blushed in response, as she ripped a piece of her donut and offered it to Sark, who accepted it, allowing her to fed him. The couple shared a knowing smile, as they remembered their operation in Ireland. It had gone terribly wrong, but they had shared an amazing night on the beach afterwards, which had made the trouble seem worth it.  
  
Taking a piece of her chocolate covered donut, she quickly placed it in her mouth before taking Sark's hand and placing it in her own, while he placed his free hand around her waist and across her swollen stomach. They walked into the conference room confidently, feeling comfortable in each other presence, looking like the perfect couple.  
  
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A/N: I don't know if anyone is going to like this chapter, but when I re- read I liked it, which is why I'm posting it. I hope you liked the S/S phone conversation. Tell me what you think, but be nice!  
  
Thank you to all my reviewers! Tell me what you think of this chapter, your suggestions are always welcome!  
  
Star Mage1: I hope that this chapter didn't disappoint you! I wasn't too sure how I should write everyone's reactions, so I just went with it.  
  
JuliansGIrl: Glad that you're happy about this fic being Sarkney! Yeah, sorry if the beginning confused you, but I'm glad that you enjoyed the rest! I have to admit that my favourite part of the first chapter was the bit with Sydney and Lauren!  
  
Actrez: lol. I was hoping that I would get that kind of reaction! I take it that you like that Sark is the father of Sydney's baby then? I hope that you keep reading!  
  
Coffeeaddict14: Thanks for adding me to your AA list! Sorry if you got alerts on other stories as well! I have a problem with starting new stories without finishing old ones. lol.  
  
TheUptownGirl: To my loyal reader. lol. Sorry to disappoint you, but I am writing some S/V stories, promise! Not that I'm advertising my own fics, or anything, lol, but if you want some S/V fluff, check out 'Paradise'. It's probably going to be a bit sad, but will be 100% S/V! PROMISE! Thanks for the review, and I'm happy that you're going to carry on reading anyways! I love that you like my stories and have me on your favourites' list! I love all my reviewers, but especially the ones who put their favourites! Thank you!  
  
Ele: Yes, this means that Sark is good, and they are 'involved'. lol. There will be some S/S fluff in this flick! And I'm open to any idea for baby names/ genders! Glad that you like what I wrote!  
  
GHCinder: I thought that it was about time that I wrote a fic that wasn't completely depressing and involved some kind of suicide attempt, lol. I'm pleased that you liked how Syd came back! I'll bring Jack into the fic at some point, but I'm not good at writing Jack scenes, so it might be a while. And yes, Sark is also working with the Covenant!  
  
Allyispy: I'm glad that you think my fic is great and the tension! Lol, I'm going to make Vaughn jealous, don't you worry! This is a Sarkney fic! And I completely agree with you, I love Sark too, but I have to say that I love Vaughn more! lol. Vaughn is pissing me off too, which is why this fic is Sarkney all the way baby! Also, thanks for having me on your favourites' list! I always smile now when I see your name on a review, so thanks!  
  
TikigirlK16: I hope that it will be an interesting fic! Thanks for you're review and sorry it took so long to update. 


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